Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009600.1 Kokia drynarioides strain JFW-HI SEQ_124316, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 28012
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 87 characters in sequence are not A, C, G, or T
Found at i:2339 original size:27 final size:22
Alignment explanation
Indices: 2286--2335 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
2276 AAATCAGATA
2286 TAAAATTATTAATAATATAATT
1 TAAAATTATTAATAATATAATT
2308 T-AAATTA-TAATAAT-TAATAT
1 TAAAATTATTAATAATATAAT-T
*
2328 TAATATTA
1 TAAAATTA
2336 AAATGAATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.16
20 9 0.36
21 11 0.44
22 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TAAAATTATTAATAATATAATT
Found at i:8797 original size:61 final size:62
Alignment explanation
Indices: 8629--8797 Score: 146
Period size: 64 Copynumber: 2.6 Consensus size: 62
8619 AGTTATGTGG
* * * * ** *
8629 TATTTAAATAATTTGATGTAATATACATAAAATATAAAATTTAAATACATTTTAAGTAATTA
1 TATTTAAATAATTTAATATAATAAACATAAAATATAAATTTTAAATACATAATAAGTAAATA
* * * *
8691 -ATATAAATTATTTGTAAAATTAATAATACATAAAATAATTTAAATTTTAAA-ATATAATAA-TA
1 TATTTAAA-TAATT-TAATA-TAATAA-ACATAAAAT-A--TAAATTTTAAATACATAATAAGTA
8753 AATA
59 AATA
8757 TATTTAAATAATTTAATATAATCAAACATAAAATATAAATT
1 TATTTAAATAATTTAATATAAT-AAACATAAAATATAAATT
8798 AGTTTAATTT
Statistics
Matches: 84, Mismatches: 14, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
61 12 0.14
62 4 0.05
63 3 0.04
64 18 0.21
65 15 0.18
66 10 0.12
67 12 0.14
68 10 0.12
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.40
Consensus pattern (62 bp):
TATTTAAATAATTTAATATAATAAACATAAAATATAAATTTTAAATACATAATAAGTAAATA
Found at i:9814 original size:49 final size:49
Alignment explanation
Indices: 9760--9858 Score: 153
Period size: 49 Copynumber: 2.0 Consensus size: 49
9750 ATTACTCAAT
*
9760 TTTATCACACTCTTAATGTGAATAAATAAAAAAAATTTATATTAAAAAA
1 TTTATCACACTCATAATGTGAATAAATAAAAAAAATTTATATTAAAAAA
* * * *
9809 TTTATCACACTCATAATGTGAATGAATGAAAATATTTTATATTAAAAAA
1 TTTATCACACTCATAATGTGAATAAATAAAAAAAATTTATATTAAAAAA
9858 T
1 T
9859 AGTTATAAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.36
Consensus pattern (49 bp):
TTTATCACACTCATAATGTGAATAAATAAAAAAAATTTATATTAAAAAA
Found at i:12631 original size:32 final size:33
Alignment explanation
Indices: 12575--12637 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
12565 ATAAATAAGA
** **
12575 TTAATCAAAATGAAATTAGGAAAATA-ACAAAT
1 TTAATCAAAACAAAATTAACAAAATATACAAAT
12607 TTAATCAAAACAAAATTAACAAAATATACAA
1 TTAATCAAAACAAAATTAACAAAATATACAA
12638 CTTTTACTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 22 0.85
33 4 0.15
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.24
Consensus pattern (33 bp):
TTAATCAAAACAAAATTAACAAAATATACAAAT
Found at i:13433 original size:129 final size:129
Alignment explanation
Indices: 13203--13518 Score: 587
Period size: 129 Copynumber: 2.4 Consensus size: 129
13193 GACCTAATCA
* * *
13203 AATCTTTTTACGCGAATTGAGAAGACAAGCCAAGCACCTCAACCTGGTTACTCAATTCGAAAAGT
1 AATCTTTTTACGCGAATTGAGATGACAAGCCAAGCACCTCAACCCGGTTACTCAATTCAAAAAGT
13268 CGGTAGCTTTATTTTTCAAGGTAGCTCGGTTAGTGGAGTGTTACAAGCTTCGGTTCGTCACTCG
66 CGGTAGCTTTATTTTTCAAGGTAGCTCGGTTAGTGGAGTGTTACAAGCTTCGGTTCGTCACTCG
13332 AATCTTTTTACGCGAATTGAGATGACAAGCCAAGCACCTCAACCCGGTTACTCAATTCAAAAAGT
1 AATCTTTTTACGCGAATTGAGATGACAAGCCAAGCACCTCAACCCGGTTACTCAATTCAAAAAGT
13397 CGGTAGCTTTATTTTTCAAGGTAGCTCGGTTAGTGGAGTGTTACAAGCTTCGGTTCGTCACTCG
66 CGGTAGCTTTATTTTTCAAGGTAGCTCGGTTAGTGGAGTGTTACAAGCTTCGGTTCGTCACTCG
* *
13461 AATATTTTTACGCGAATTAAGATGACAAGCCAAGCACCTCAACCCGGTTACTCAATTC
1 AATCTTTTTACGCGAATTGAGATGACAAGCCAAGCACCTCAACCCGGTTACTCAATTC
13519 GGTCACATTT
Statistics
Matches: 182, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
129 182 1.00
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (129 bp):
AATCTTTTTACGCGAATTGAGATGACAAGCCAAGCACCTCAACCCGGTTACTCAATTCAAAAAGT
CGGTAGCTTTATTTTTCAAGGTAGCTCGGTTAGTGGAGTGTTACAAGCTTCGGTTCGTCACTCG
Found at i:22880 original size:21 final size:21
Alignment explanation
Indices: 22854--22922 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
22844 TGCTTCACAA
22854 AATCCAAGTACATCTTAATTG
1 AATCCAAGTACATCTTAATTG
*
22875 AATCCAAGT-CA-CTTTATT-
1 AATCCAAGTACATCTTAATTG
*
22893 TATCCAAGTACATCTTAATTG
1 AATCCAAGTACATCTTAATTG
22914 AATCCAAGT
1 AATCCAAGT
22923 CACTTTATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 8 0.20
19 8 0.20
20 8 0.20
21 17 0.41
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (21 bp):
AATCCAAGTACATCTTAATTG
Found at i:22909 original size:39 final size:39
Alignment explanation
Indices: 22855--22934 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
22845 GCTTCACAAA
22855 ATCCAAGTACATCTTAATTGAATCCAAGTCACTTTATTT
1 ATCCAAGTACATCTTAATTGAATCCAAGTCACTTTATTT
22894 ATCCAAGTACATCTTAATTGAATCCAAGTCACTTTATTT
1 ATCCAAGTACATCTTAATTGAATCCAAGTCACTTTATTT
22933 AT
1 AT
22935 ACACAATTGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (39 bp):
ATCCAAGTACATCTTAATTGAATCCAAGTCACTTTATTT
Found at i:23040 original size:33 final size:33
Alignment explanation
Indices: 22994--23075 Score: 87
Period size: 32 Copynumber: 2.5 Consensus size: 33
22984 CTATTTACTT
* * *
22994 AAAATAA-ATAATTTTAGTCAAAATAAAATTAGC
1 AAAATAACA-AATTTTAATCAAAACAAAATTAAC
*
23027 AAAATAACAAA-TTTAATCAAAACAAAATTAAT
1 AAAATAACAAATTTTAATCAAAACAAAATTAAC
*
23059 AAAATAAACAACTTTTA
1 AAAAT-AACAAATTTTA
23076 CTAAGCTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
32 22 0.54
33 14 0.34
34 5 0.12
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.28
Consensus pattern (33 bp):
AAAATAACAAATTTTAATCAAAACAAAATTAAC
Done.